Triplexes with 8-aza-2′-deoxyisoguanosine replacing protonated dC: Probing third strand stability with a fluorescent nucleobase targeting duplex DNA

ChemBioChem

Volumn 11, Issue 10, 2010, Pages 1443-1450

  Seela, Frank ^a,b   Jiang, Dawei ^a,c   Budow, Simone ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b UNIVERSITY OF OSNABRÜCK   (Germany)

^c SICHUAN UNIVERSITY   (China)

Author keywords

DNA; Fluorescent probes; Mismatch discrimination; Modified oligonucleotides; Triplex DNA

Indexed keywords

2' DEOXYISOGUANOSINE; 8 AZA 2' DEOXYISOGUANOSINE; DOUBLE STRANDED DNA; NUCLEIC ACID BASE; OLIGONUCLEOTIDE; PURINE NUCLEOSIDE; UNCLASSIFIED DRUG; 8-AZA-2'-DEOXYISOGUANOSINE; DEOXYCYTIDINE PHOSPHATE; DEOXYGUANOSINE; DNA; FLUORESCENT DYE; TRIPLEX DNA;

ALKALINITY; ARTICLE; BASE PAIRING; DISSOCIATION; DNA BINDING; DNA HYBRIDIZATION; DNA STRAND; FLUORESCENCE; GENE TARGETING; MOLECULAR STABILITY; OLIGONUCLEOTIDE PROBE; PH; PRIORITY JOURNAL; PROTON TRANSPORT; ANALOGS AND DERIVATIVES; BASE MISPAIRING; CHEMISTRY; TEMPERATURE; ULTRAVIOLET SPECTROPHOTOMETRY;

BASE PAIR MISMATCH; DEOXYCYTOSINE NUCLEOTIDES; DEOXYGUANOSINE; DNA; FLUORESCENT DYES; SPECTROPHOTOMETRY, ULTRAVIOLET; TEMPERATURE;

EID: 77954378428     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.201000162     Document Type: Article

References (63)

1. a) M. Faria, C. Giovannangeli, J. Gene Med. 2001, 3, 299-310;
2. b) K. M. Vasquez, P. M. Glazer, Q. Rev. Biophys. 2002, 35, 89-107.
3. N. T. Thuong, C. Hélène, Angew. Chem. 1993, 105, 697-723;
4. Angew. Chem. Int. Ed. Engl. 1993, 32, 666-690.
5. M. D. Frank-Kamenetskii, S. M. Mirkin, Annu. Rev. Biochem. 1995, 64, 65-95.
6. S. O. Doronina, J.-P. Behr, Chem. Soc. Rev. 1997, 26, 63-71.
7. H. E. Moser, P. B. Dervan, Science 1987, 238, 645-650.
8. G. Felsenfeld, D. R. Davies, A. Rich, J. Am. Chem. Soc. 1957, 79, 2023-2024.
9. a) C. Hélène, Anticaner Drug Des. 1991, 6, 569-584;
10. b) C. Hélène, T. Garestier, C. Giovannangeli, J.-S. Sun, Gene Ther. Mol. Biol. 1998, 1, 467-474.
11. a) P. P. Chan, P. M. Glazer, J. Mol. Med. 1997, 75, 267-282;
12. b) A. Jain, M. Magistri, S. Napoli, G. M. Carbone, C. V. Catapano, Biochemie 2010, 92, 317-320.
13. a) M. F. Jacobsen, J. B. Ravnsbæk, K. V. Gothelf, Org. Biomol. Chem. 2010, 8, 50-52;
14. b) M. S. Han, A. K. R. Lytton-Jean, C. A. Mirkin, J. Am. Chem. Soc. 2006, 128, 4954-4955;
15. c) X. Zhu, Y. Liu, J. Yang, Z. Liang, G. Li, Biosens. Bioelectron. 2010, 25, 2135-2139;
16. d) Y. Chen, S.-H. Lee, C. Mao, Angew. Chem. 2004, 116, 5449-5452.
17. a) I. Trkulja, R. Häner, J. Am. Chem. Soc. 2007, 129, 7982-7989;
18. b) J. Schwarz-Finsterle, S. Stein, C. Großmann, E. Schmitt, L. Trakhtenbrot, G. Rechavi, N. Amariglio, C. Cremer, M. Hausmann, J. Biochem. Biophys. Methods 2007, 70, 397-406.
19. L. Van Meervelt, D. Vlieghe, A. Dautant, B. Gallois, G. Précigoux, O. Kennard, Nature 1995, 374, 742-744.
20. J. F. Milligan, S. H. Krawczyk, S. Wadwani, M. D. Matteucci, Nucleic Acids Res. 1993, 21, 327-333.
21. L. E. Xodo, G. Manzini, F. Quadrifoglio, G. A. van der Marel, J. H. van Boom, Nucleic Acids Res. 1991, 19, 5625-5631.
22. G. Xiang, W. Soussou, L. W. McLaughlin, J. Am. Chem. Soc. 1994, 116, 11155-11156.
23. A. K. Phipps, M. Tarköy, P. Schultze, J. Feigon, Biochemistry 1998, 37, 5820-5830.
24. L. Lacroix, J. Lacoste, J. F. Reddoch, J.-L. Mergny, D. D. Levy, M. M. Seidman, M. D. Matteucci, P. M. Glazer, Biochemistry 1999, 38, 1893-1901.
25. S. D. Osborne, V. E. C. Powers, D. A. Rusling, O. Lack, K. R. Fox, T. Brown, Nucleic Acids Res. 2004, 32, 4439-4447.
26. a) D. A. Barawkar, K. G. Rajeev, V. A. Kumar, K. N. Ganesh, Nucleic Acids Res. 1996, 24, 1229-1237;
27. b) K. G. Rajeev, V. R. Jadhav, K. N. Ganesh, Nucleic Acids Res. 1997, 25, 4187-4193.
28. S. Hildbrand, A. Blaser, S. P. Parel, C. J. Leumann, J. Am. Chem. Soc. 1997, 119, 5499-5511.
29. U. Parsch, J. W. Engels, Chem. Eur. J. 2000, 6, 2409-2424.
30. M. Mills, P. B. Arimondo, L. Lacroix, T. Garestier, H. Klump, J.-L. Mergny, Biochemistry 2002, 41, 357-366.
31. J. S. Koh, P. B. Dervan, J. Am. Chem. Soc. 1992, 114, 1470-1478.
32. H. Brunar, P. B. Dervan, Nucleic Acids Res. 1996, 24, 1987-1991.
33. F. Seela, K. I. Shaikh, T. Wiglenda, P. Leonard, Helv. Chim. Acta 2004, 87, 2507-2516.
34. a) F. Seela, K. I. Shaikh, T. Wiglenda, Helv. Chim. Acta 2006, 89, 598-613;
35. b) F. Seela, K. I. Shaikh, Org. Biomol. Chem. 2006, 4, 3993-4004.
36. P. S. Miller, G. Bi, S. A. Kipp, V. Fok, R. K. DeLong, Nucleic Acids Res. 1996, 24, 730-736.
37. A. Mayer, A. Häberli, C. J. Leumann, Org. Biomol. Chem. 2005, 3, 1653-1658.
38. T. J. Povsic, P. B. Dervan, J. Am. Chem. Soc. 1989, 111, 3059-3061.
39. a) F. Seela, C. Wei, Helv. Chim. Acta 1997, 80, 73-85;
40. b) F. Seela, Y. He, C. Wei, Tetrahedron 1999, 55, 9481-9500;
41. c) H. Sugiyama, S. Ikeda, I. Saito, J. Am. Chem. Soc. 1996, 118, 9994-9995.
42. Z. Kazimierczuk, R. Mertens, W. Kawczynski, F. Seela, Helv. Chim. Acta 1991, 74, 1742-1748.
43. D. Jiang, F. Seela, J. Am. Chem. Soc. 2010, 132, 4016-4024.
44. a) E. Bédu, R. Benhida, M. Devys, J.-L. Fourrey, Tetrahedron Lett. 1999, 40, 835-838;
45. b) S. Dorner, C. Panuschka, W. Schmid, A. Barta, Nucleic Acids Res. 2003, 31, 6536-6542.
46. J. S. Lee, D. A. Johnson, A. R. Morgan, Nucleic Acids Res. 1979, 6, 3073-3091.
47. G. E. Plum, Y.-W. Park, S. F. Singleton, P. B. Dervan, K. J. Breslauer, Proc. Natl. Acad. Sci. USA 1990, 87, 9436-9440.
48. I. Van Daele, N. Bomholt, V. V. Filichev, S. Van Calenbergh, E. B. Pedersen, ChemBioChem 2008, 9, 791-801.
49. I. Trkulja, S. M. Biner, S. M. Langenegger, R. Häner, ChemBioChem 2007, 8, 25-27.
50. a) C. M. McKeen, L. J. Brown, J. T. G. Nicol, J. M. Mellor, T. Brown, Org. Biomol. Chem. 2003, 1, 2267-2275;
51. b) R. A. J. Darby, M. Sollogoub, C. McKeen, L. Brown, A. Risitano, N. Brown, C. Barton, T. Brown, K. R. Fox, Nucleic Acids Res. 2002, 30, e39;
52. c) Y. Xiao, K. J. I. Plakos, X. Lou, R. J. White, J. Qian, K. W. Plaxco, H. T. Soh, Angew. Chem. 2009, 121, 4418-4422;
53. Angew. Chem. Int. Ed. 2009, 48, 4354-4358.
54. a) P. V. Scaria, R. H. Shafer, J. Biol. Chem. 1991, 266, 5417-5423;
55. b) J.-L. Mergny, D. Collier, M. Rougée, T. Montenay-Garestier, C. Hélène, Nucleic Acids Res. 1991, 19, 1521-1526.
56. F. Godde, K. Aupeix, S. Moreau, J.-J. Toulmé, Antisense Nucleic Acid Drug Dev. 1998, 8, 469-476.
57. A. K. Shchyolkina, D. N. Kaluzhny, O. F. Borisova, M. E. Hawkins, R. L. Jernigan, T. M. Jovin, D. J. Arndt-Jovin, V. B. Zhurkin, Nucleic Acids Res. 2004, 32, 432-440.
58. V. Zozulya, A. Shcherbakova, I. Dubey, J. Fluoresc. 2000, 10, 49-53.
59. J.-S. Sun, J.-L. Mergny, R. Lavery, T. Montenay-Garestier, C. Hélène, J. Biomol. Struct. Dyn. 1991, 9, 411-424.
60. D. A. Rusling, T. Brown, K. R. Fox, Biophys. Chem. 2006, 123, 134-140.
61. F. Seela, H. Driller, Nucleic Acids Res. 1986, 14, 2319-2332.
62. a) K. J. Hampel, P. Crosson, J. S. Lee, Biochemistry 1991, 30, 4455-4459;
63. b) T. Thomas, T. J. Thomas, Biochemistry 1993, 32, 14068-14074.